POLR2G RNA-Seq in K562

General Information


RBP	POLR2G
Cell_Line	K562
Method	CRISPR
Exp_Name	POLR2G-BGKcLV06-K562
ENCODE_series_ID	ENCSR044VMR
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR580TGX
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	POLR2G-BGKcLV06-25
Rep2	POLR2G-BGKcLV06-26
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	52.7
Rep2_qPCR	49.2
Rep1_WB	61.0
Rep2_WB	77.7
Antibody Cat#	GTX108874
Antibody Lot#
Antibody DCC ID	ENCAB392AZR
Status	Released
Project	ENCODE3
ID	775

Experiment Information (Status: Released)

	BGKcLV06-25	BGKcLV06-26
idx	201	202
TRCN#_or_BGC#	BGC#0000080	BGC#0000080
shRNA_or_gRNA_sequence	AAGTTGGGGCCGAAGTAGCG	AAGTTGGGGCCGAAGTAGCG
PAM
Name	POLR2G_91	POLR2G_91
Sample_ID	BGKcLV06-25	BGKcLV06-26
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	POLR2G	POLR2G
qPCR_result	52.7	49.2
Ave_qPCR	51.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	1376	1628
WB_result	61.0	77.7
Ave_WB	69.3
WB_DONE_date	6/29/17
MW	19kD
IP
antibody_Cat#	GTX108874
Antibody DCC ID	ENCAB392AZR	ENCAB392AZR
submitted_to_DCC_date	9/29/17
Rep1_TPM	172.4	0
Rep2_TPM	149.4	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4299	4300

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
POLR2G	Product_ID: GTX108874 Lot_ID: 40023 Source: GeneTex Target Name: POLR2G-human

Experiment Status

	BGKcLV06-25	BGKcLV06-26
Sample_ID	BGKcLV06-25	BGKcLV06-26
Sample Name	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-26
Sample Name	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-26
RBP	POLR2G	POLR2G
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1367	1368

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-25	BGKcLV06-26
Sample #
Sample Name	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-26
Sample_Name_Alias	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-26
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/A2.png	DNA_Library_set39/set2/B2.png
RIN	9.9	9.0
libSample_RNA_Well	RNA_Library_set39/set3/A2.png	RNA_Library_set39/set3/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-25	BGKcLV06-26
RBP	POLR2G	POLR2G
Batch_ID	BGKcLV06	BGKcLV06
WB_result	61.000	77.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3062	3063

Sequencing Information

	BGKcLV06-25	BGKcLV06-26
Sample_ID	BGKcLV06-25	BGKcLV06-26
Sample Name	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-26
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	57,767,084	43,884,810
total_aligned_reads	49,866,636	39,074,976
unique_aligned_reads	45,079,256	35,272,606
percent_uniqueAligned	0.78036	0.80375
correlation_replicates	0.987043	0.987043
spikein_reads	28,660	24,824
percent_spikeins	0.00050	0.00057
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1713	1714

Data Submission Information

	BGKcLV06-25	BGKcLV06-25
ENCODE_alias	brenton-graveley:POLR2G-BGKcLV06	brenton-graveley:POLR2G-BGKcLV06-K562
ENCODE_accession	ENCSR580TGX	ENCSR044VMR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-25	BGKcLV06-25
Sample Name	POLR2G-BGKcLV06-25	POLR2G-BGKcLV06-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3223	6861

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1713	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22478
POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1713	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22514
POLR2G-BGKcLV06-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R1.fastq.gz,POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22550
POLR2G-BGKcLV06-25_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25/Aligned.sortedByCoord.out.bam		ENCORE2	22586
POLR2G-BGKcLV06-25_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25/Aligned.sortedByCoord.out.bam		ENCORE2	22622
POLR2G-BGKcLV06-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25/Aligned.sortedByCoord.out.bam		ENCORE2	22658
POLR2G-BGKcLV06-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25/Aligned.sortedByCoord.out.bam		ENCORE2	22694
POLR2G-BGKcLV06-25_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1713					GRCh38	V40	POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R1.fastq.gz,POLR2G-BGKcLV06-25_GTCCGC_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22730
POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1714	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22479
POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1714	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22515
POLR2G-BGKcLV06-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R1.fastq.gz,POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22551
POLR2G-BGKcLV06-26_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26/Aligned.sortedByCoord.out.bam		ENCORE2	22587
POLR2G-BGKcLV06-26_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26/Aligned.sortedByCoord.out.bam		ENCORE2	22623
POLR2G-BGKcLV06-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26/Aligned.sortedByCoord.out.bam		ENCORE2	22659
POLR2G-BGKcLV06-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26/Aligned.sortedByCoord.out.bam		ENCORE2	22695
POLR2G-BGKcLV06-26_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1714					GRCh38	V40	POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R1.fastq.gz,POLR2G-BGKcLV06-26_GTGAAA_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22731